Abstract
Curtobacterium sp. strain WW7 is a Gram-positive, non-motile, orange rod-shaped bacterium isolated from branches of wild willow (Salix sitchensis) trees. The WW7T strain has optimum growth in the temperature range between 25 and 30 °C, a pH range of 6–7.7, and tolerates up to 5.5% (w/v) of NaCl. The genome sequencing of strain WW7T revealed a genome size of approximately 3.8 Mbp and a G + C content of 71.3 mol%. The phylogenomic analyses support the WW7T affiliation to a novel Curtobacterium lineage, with Curtobacterium herbarum being the closest type-strain. Chemotaxonomic analysis indicates that the carbon sources assimilation profile of strain WW7T was similar to the type strains, i.e. Curtobacterium luteum, Curtobacterium albidum, and Curtobacterium flaccumfaciens, while no assimilation of the organic acids succinate, alpha-ketobutyrate, mono methyl-succinate, and lactate was observed. Finally, fatty acid methyl ester analysis identifies anteiso-C15:0 and anteiso-C17:0 as major cellular fatty acids which is a common feature for members of the Curtobacterium genus. Based on the results of phylogenomic and chemotaxonomic analyses, strain WW7T represents a novel Curtobacterium lineage, for which the name Curtobacterium salicis sp. nov. is proposed. The type strain is WW7T (DSM 34805T-NRRL B-68078T).
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Data availability
Strain WW7T genome sequence and annotation have been submitted to the NCBI Assembly database under the accession number GCF_011759505.1. The partial 16S rRNA gene sequence of the WW7T strain has been deposited to the NCBI Nucleotide database with the accession number KU523564.1. Strain WW7T culture are available in the Agricultural Research Culture Collection (NRRL) and German Collection of Microorganisms and Cell Cultures (DSMZ) under the accession codes NRRL B-68078T and DSM 34805T, respectively.
Code availability
Agricultural Research Culture Collection (NRRL) code NRRL B-68078. German Collection of Microorganisms and Cell Cultures (DSMZ) code DSM 34805.
Abbreviations
- dDDH:
-
Digital DNA–DNA hybridization
- FA:
-
Fatty acid
- FAME:
-
Fatty acid methyl ester analysis
- GTDB-tk:
-
Genome taxonomy database
- MS:
-
Murashige and Skoog
- TYGS:
-
Type-strain genome server
- PM:
-
Phenotype microarray
References
Aizawa T, Ve NB, Kimoto KI et al (2007) Curtobacterium ammoniigenes sp. nov., an ammonia-producing bacterium isolated from plants inhabiting acidic swamps in actual acid sulfate soil areas of Vietnam. Int J Syst Evol Microbiol 57:1447–1452. https://doi.org/10.1099/IJS.0.64731-0
Alves LPS, do Amaral FP, Kim D et al (2019) Importance of poly-3-hydroxybutyrate metabolism to the ability of Herbaspirillum seropedicae to promote plant growth. Appl Environ Microbiol. https://doi.org/10.1128/AEM.02586-18
Angelosi GA, Abest E, Martinetti G, Nester EW (1991) Genetic analysis of Agrobacterium. Methods Enzymol 204:384–397. https://doi.org/10.1016/0076-6879(91)04020-O
Aramaki T, Blanc-Mathieu R, Endo H et al (2020) KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36:2251–2252. https://doi.org/10.1093/BIOINFORMATICS/BTZ859
Bankevich A, Nurk S, Antipov D et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455. https://doi.org/10.1089/CMB.2012.0021
Behrendt U, Ulrich A, Schumann P et al (2002) Diversity of grass-associated Microbacteriaceae isolated from the phyllosphere and litter layer after mulching the sward; polyphasic characterization of Subtercola pratensis sp. nov., Curtobacterium herbarum sp. nov. and Plantibacter flavus gen. nov., sp. nov. Int J Syst Evol Microbiol 52:1441–1454. https://doi.org/10.1099/00207713-52-5-1441
Borisov VB, Siletsky SA, Paiardini A et al (2021) Bacterial oxidases of the cytochrome bd family: redox enzymes of unique structure, function, and utility as drug targets. Antioxid Redox Signal 34:1280. https://doi.org/10.1089/ARS.2020.8039
Chandel A, Mann R, Kaur J et al (2022) Australian native Glycine clandestina seed microbiota hosts a more diverse bacterial community than the domesticated soybean Glycine max. Environ Microbiome. https://doi.org/10.1186/S40793-022-00452-Y
Chase AB, Arevalo P, Polz MF et al (2016) Evidence for ecological flexibility in the cosmopolitan genus Curtobacterium. Front Microbiol 7:1874. https://doi.org/10.3389/FMICB.2016.01874/BIBTEX
Chen G, Khojasteh M, Taheri-Dehkordi A et al (2021) Complete genome sequencing provides novel insight into the virulence repertories and phylogenetic position of dry beans pathogen Curtobacterium flaccumfaciens pv. flaccumfaciens. Phytopathology 111:268–280. https://doi.org/10.1094/PHYTO-06-20-0243-R
Doty SL, Oakley B, Xin G et al (2009) Diazotrophic endophytes of native black cottonwood and willow. Symbiosis 47:23–33. https://doi.org/10.1007/BF03179967/METRICS
Eren AM, Kiefl E, Shaiber A et al (2020) Community-led, integrated, reproducible multi-omics with Anvi’o. Nat Microbiol 6(1):3–6. https://doi.org/10.1038/s41564-020-00834-3
Evseev P, Lukianova A, Tarakanov R et al (2022) Curtobacterium spp. and Curtobacterium flaccumfaciens: phylogeny, genomics-based taxonomy, pathogenicity, and diagnostics. Curr Issues Mol Biol 44:889–927. https://doi.org/10.3390/CIMB44020060/S1
Feng GD, Li J, Yang S et al (2023) Curtobacterium caseinilyticum sp. nov., Curtobacterium subtropicum sp. nov. and Curtobacterium citri sp. nov., isolated from citrus phyllosphere. Int J Syst Evol Microbiol. https://doi.org/10.1099/IJSEM.0.006152
Firrincieli A, Khorasani M, Frank AC, Doty SL (2020) Influences of climate on phyllosphere endophytic bacterial communities of wild poplar. Front Plant Sci. https://doi.org/10.3389/FPLS.2020.00203
Francis MJ, Doherty RR, Patel M et al (2011) Curtobacterium flaccumfaciens septic arthritis following puncture with a Coxspur Hawthorn thorn. J Clin Microbiol 49:2759–2760. https://doi.org/10.1128/JCM.00340-11
Kandel SL, Firrincieli A, Joubert PM et al (2017) An in vitro study of bio-control and plant growth promotion potential of salicaceae endophytes. Front Microbiol. https://doi.org/10.3389/FMICB.2017.00386
Kim MK, Kim YJ, Bin KH et al (2008) Curtobacterium ginsengisoli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 58:2393–2397. https://doi.org/10.1099/IJS.0.65591-0
Li W, O’Neill KR, Haft DH et al (2021) RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation. Nucleic Acids Res 49:D1020–D1028. https://doi.org/10.1093/NAR/GKAA1105
Meier-Kolthoff JP, Göker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 10(1):1–10. https://doi.org/10.1038/s41467-019-10210-3
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform. https://doi.org/10.1186/1471-2105-14-60
Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32:268–274. https://doi.org/10.1093/MOLBEV/MSU300
Osdaghi E, Taghavi SM, Calamai S et al (2018) Phenotypic and molecular-phylogenetic analysis provide novel insights into the diversity of Curtobacterium flaccumfaciens. Phytopathology 108:1154–1164. https://doi.org/10.1094/PHYTO-12-17-0420-R
Parks DH, Chuvochina M, Rinke C et al (2022) GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res 50:D785–D794. https://doi.org/10.1093/NAR/GKAB776
Rennie RJ (1981) A single medium for the isolation of acetylene-reducing (dinitrogen-fixing) bacteria from soils. Can J Microbiol 27:8–14. https://doi.org/10.1139/M81-002
Scales NC, Chase AB, Finks SS et al (2022) Differential response of bacterial microdiversity to simulated global change. Appl Environ Microbiol. https://doi.org/10.1128/AEM.02429-21/SUPPL_FILE/AEM.02429-21-S0001.PDF
Sivakumar N, Sathishkumar R, Selvakumar G et al (2020) Phyllospheric microbiomes: diversity, ecological significance, and biotechnological applications. Plant Microbiomes Sustain Agricult 25:113. https://doi.org/10.1007/978-3-030-38453-1_5
South KA, Nordstedt NP, Jones ML (2021) Identification of plant growth promoting rhizobacteria that improve the performance of greenhouse-grown petunias under low fertility conditions. Plants. https://doi.org/10.3390/PLANTS10071410
Varga T, Hixson KK, Ahkami AH et al (2020) Endophyte-promoted phosphorus solubilization in populus. Front Plant Sci 11:1585. https://doi.org/10.3389/FPLS.2020.567918/BIBTEX
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JF conceived the experiments with help from AF. AF conducted the genomic and bioinformatics analyses. JF and DB conducted chemotaxonomic analyses. SLD isolated the strain. All authors contributed to writing the manuscript.
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Intrinsyx Bio is developing agricultural products based on the microbial strain in this study.
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Freeman, J., Firrincieli, A., Baker, D. et al. Curtobacterium salicis sp. nov., isolated from willow tree stems in Washington state. Antonie van Leeuwenhoek 117, 62 (2024). https://doi.org/10.1007/s10482-024-01956-y
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DOI: https://doi.org/10.1007/s10482-024-01956-y